Question: (Closed) Command Line in Galaxy
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gravatar for caluga61
2.5 years ago by
caluga610
Mississippi
caluga610 wrote:

I am new to Galaxy and NGS data analysis in general. I was wondering, is there a way to view the command line commands that are running the Galaxy tools? For instance if I run Bowtie2 in Galaxy, is there a way to see how that instance of Bowtie2 would look if ran from command line? Thanks for any input.

command line • 1.1k views
ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.5 years ago by caluga610

Does not appear that you can (any longer?). At least on PSU galaxy. I see that you have posted this question over on Galaxy Biostars as well (was going to suggest that).

ADD REPLYlink written 2.5 years ago by genomax65k

I came across this older post: https://biostar.usegalaxy.org/p/6493/#6522. Does anyone know how to purposely cause a tool to fail?

ADD REPLYlink written 2.5 years ago by caluga610

Bad input can sometimes do the trick since many programs don't check/validate their input (but Galaxy may do it for them instead though)

ADD REPLYlink written 2.5 years ago by Jean-Karim Heriche18k

Normally you have to be logged in as an admin for that to appear. I agree this is annoying. In fact, it even bothers me as an admin since I sometimes have to "impersonate" users (i.e., run Galaxy as them) in order to debug things...but then I can no longer see the commands getting sent to the queue without using ssh (or a different browser). If I remember I'll ask someone tomorrow about this, since I'm at a Galaxy conference at the moment.

ADD REPLYlink written 2.5 years ago by Devon Ryan89k

Hello caluga61!

We believe that this post does not fit the main topic of this site.

Better place to ask this: https://biostar.usegalaxy.org

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 22 months ago by Michael Dondrup46k
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